Nichols NN, Sutivisedsak N, Dien BS, Biswas A, Lesch WC, Cotta MA. Conversion of starch from dry common beans (Phaseolus vulgaris L.) to ethanol. Ind Crop Prod. 2011. https://doi.org/10.1016/j.indcrop.2010.12.029.
Lee SC, Gepts PL, Whitaker JR. Protein structures of common bean (Phaseolus vulgaris) alpha-amylase inhibitors. J Agric Food Chem. 2002. https://doi.org/10.1021/jf020189t.
Singh RS, Walia AK. Microbial lectins and their prospective mitogenic potential. Crit Rev Microbiol. 2014. https://doi.org/10.3109/1040841x.2012.733680.
Delgado-Salinas A, Turley T, Richman A, Lavin M. Phylogenetic analysis of the cultivated and wild species of Phaseolus (Fabaceae). Syst Bot. 1999. https://doi.org/10.2307/2419699.
Ohama N, Sato H, Shinozaki K, Yamaguchi-Shinozaki K. Transcriptional regulatory network of plant heat stress response. Trends Plant Sci. 2017. https://doi.org/10.1016/j.tplants.2016.08.015.
Scharf KD, Rose S, Zott W, Schöffl F, Nover L. Three tomato genes code for heat stress transcription factors with a region of remarkable homology to the DNA-binding domain of the yeast HSF. EMBO J. 1990. https://doi.org/10.1002/j.1460-2075.1990.tb07900.x.
Scharf KD, Berberich T, Ebersberger I, Nover L. The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim Biophys Acta. 2012. https://doi.org/10.1016/j.bbagrm.2011.10.002.
Wu C. Heat shock transcription factors: structure and regulation. Annu Rev Cell Dev Biol. 1995. https://doi.org/10.1146/annurev.cb.11.110195.002301.
Fragkostefanakis S, Röth S, Schleiff E, Scharf KD. Prospects of engineering thermotolerance in crops through modulation of heat stress transcription factor and heat shock protein networks. Plant Cell Environ. 2015. https://doi.org/10.1111/pce.12396.
Bharti K, Von Koskull-Döring P, Bharti S, Kumar P, Tintschl-Körbitzer A, Treuter E, et al. Tomato heat stress transcription factor HsfB1 represents a novel type of general transcription coactivator with a histone-like motif interacting with the plant CREB binding protein ortholog HAC1. Plant Cell. 2004. https://doi.org/10.1105/tpc.019927.
Busch W, Wunderlich M, Schöffl F. Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J. 2005. https://doi.org/10.1111/j.1365-313X.2004.02272.x.
Guo J, Wu J, Ji Q, Wang C, Luo L, Yuan Y, et al. Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis. J Genet Genomics. 2008. https://doi.org/10.1016/s1673-8527(08)60016-8.
Chung E, Kim KM, Lee JH. Genome-wide analysis and molecular characterization of heat shock transcription factor family in Glycine max. J Genet Genomics. 2013. https://doi.org/10.1016/j.jgg.2012.12.002.
Lin YX, Jiang HY, Chu ZX, Tang XL, Zhu SW, Cheng BJ. Genome-wide identification, classification and analysis of heat shock transcription factor family in maize. BMC Genomics. 2011. https://doi.org/10.1186/1471-2164-12-76.
Prieto-Dapena P, Almoguera C, Personat JM, Merchan F, Jordano J. Seed-specific transcription factor HSFA9 links late embryogenesis and early photomorphogenesis. J Exp Bot. 2017. https://doi.org/10.1093/jxb/erx020.
Lin Q, Jiang Q, Lin J, Wang D, Li S, Liu C, et al. Heat shock transcription factors expression during fruit development and under hot air stress in Ponkan (Citrus reticulata Blanco cv. Ponkan) fruit. Gene. 2015. https://doi.org/10.1016/j.gene.2015.01.024.
Liu M, Ma Z, Zheng T, Wang J, Huang L, Sun W, et al. The potential role of Auxin and Abscisic acid balance and FtARF2 in the final size determination of Tartary buckwheat fruit. Int J Mol Sci. 2018. https://doi.org/10.3390/ijms19092755.
Huang Y, Li MY, Wang F, Xu ZS, Huang W, Wang GL, et al. Heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress. Mol Biol Rep. 2015. https://doi.org/10.1007/s11033-014-3826-x.
Huang YC, Niu CY, Yang CR, Jinn TL. The heat stress factor HSFA6b connects ABA signaling and ABA-mediated heat responses. Plant Physiol. 2016. https://doi.org/10.1104/pp.16.00860.
Zhang J, Jia H, Li J, Li Y, Lu M, Hu J. Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar. Sci Rep. 2016. https://doi.org/10.1038/srep30050.
Liu M, Huang Q, Sun W, Ma Z, Huang L, Wu Q, et al. Genome-wide investigation of the heat shock transcription factor (Hsf) gene family in Tartary buckwheat (Fagopyrum tataricum). BMC Genomics. 2019. https://doi.org/10.1186/s12864-019-6205-0.
Wang F, Dong Q, Jiang H, Zhu S, Chen B, Xiang Y. Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula. Mol Biol Rep. 2012. https://doi.org/10.1007/s11033-011-0933-9.
Nover L, Bharti K, Döring P, Mishra SK, Ganguli A, Scharf KD. Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? Cell Stress Chaperones. 2001. https://doi.org/10.1379/1466-1268(2001)006<0177:aathst>2.0.co;2.
Liu G, Chai F, Wang Y, Jiang J, Duan W, Wang Y, et al. Genome-wide identification and classification of HSF family in grape, and their transcriptional analysis under heat acclimation and heat stress. Horticult Plant J. 2018. https://doi.org/10.1016/j.hpj.2018.06.001.
Davletova S, Rizhsky L, Liang H, Shengqiang Z, Oliver DJ, Coutu J, et al. Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis. Plant Cell. 2005. https://doi.org/10.1105/tpc.104.026971.
Zhang J, Liu B, Li J, Zhang L, Wang Y, Zheng H, et al. Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses. BMC Genomics. 2015. https://doi.org/10.1186/s12864-015-1398-3.
Wang J, Sun N, Deng T, Zhang L, Zuo K. Genome-wide cloning, identification, classification and functional analysis of cotton heat shock transcription factors in cotton (Gossypium hirsutum). BMC Genomics. 2014. https://doi.org/10.1186/1471-2164-15-961.
Tan B, Yan L, Li H, Lian X, Cheng J, Wang W, et al. Genome-wide identification of HSF family in peach and functional analysis of PpHSF5 involvement in root and aerial organ development. PeerJ. 2021. https://doi.org/10.7717/peerj.10961.
Shaul O. How introns enhance gene expression. Int J Biochem Cell Biol. 2017. https://doi.org/10.1016/j.biocel.2017.06.016.
Li Y, Chen D, Luo S, Zhu Y, Jia X, Duan Y, et al. Intron-mediated regulation of β-tubulin genes expression affects the sensitivity to carbendazim in Fusarium graminearum. Curr Genet. 2019. https://doi.org/10.1007/s00294-019-00960-4.
Li PS, Yu TF, He GH, Chen M, Zhou YB, Chai SC, et al. Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. BMC Genomics. 2014. https://doi.org/10.1186/1471-2164-15-1009.
Zhou L, Yu X, Wang D, Li L, Zhou W, Zhang Q, et al. Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum. PeerJ. 2021. https://doi.org/10.7717/peerj.11345.
Rehman A, Atif RM, Azhar MT, Peng Z, Li H, Qin G, et al. X., genome wide identification, classification and functional characterization of heat shock transcription factors in cultivated and ancestral cottons (Gossypium spp.). Int J Biol Macromol. 2021. https://doi.org/10.1016/j.ijbiomac.2021.05.016.
Zhang H, Li G, Fu C, Duan S, Hu D, Guo X. Genome-wide identification, transcriptome analysis and alternative splicing events of Hsf family genes in maize. Sci Rep. 2020. https://doi.org/10.1038/s41598-020-65068-z.
Huang B, Huang Z, Ma R, Chen J, Zhang Z, Yrjälä K. Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis). Sci Rep. 2021. https://doi.org/10.1038/s41598-021-95899-3.
Shen C, Yuan J. Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata). BMC Plant Biol. 2020. https://doi.org/10.1186/s12870-020-02683-y.
Zhang X, Xu W, Ni D, Wang M, Guo G. Genome-wide characterization of tea plant (Camellia sinensis) Hsf transcription factor family and role of CsHsfA2 in heat tolerance. BMC Plant Biol. 2020. https://doi.org/10.1186/s12870-020-02462-9.
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002. https://doi.org/10.1093/nar/30.1.325.
Li W, Wan XL, Yu JY, Wang KL, Zhang J. Genome-wide identification, classification, and expression analysis of the Hsf gene family in carnation (Dianthus caryophyllus). Int J Mol Sci. 2019. https://doi.org/10.3390/ijms20205233.
Li M, Xie F, Li Y, Gong L, Luo Y, Zhang Y, et al. Genome-wide analysis of the heat shock transcription factor gene family in Brassica juncea: structure, evolution, and expression profiles. DNA Cell Biol. 2020. https://doi.org/10.1089/dna.2020.5922.
Sarry JE, Kuhn L, Ducruix C, Lafaye A, Junot C, Hugouvieux V, et al. The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses. Proteomics. 2006. https://doi.org/10.1002/pmic.200500543.
Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, et al. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol. 2010. https://doi.org/10.1186/gb-2010-11-8-r85.
Tang R, Zhu W, Song X, Lin X, Cai J, Wang M, et al. Genome-wide identification and function analyses of heat shock transcription factors in potato. Front Plant Sci. 2016. https://doi.org/10.3389/fpls.2016.00490.
Fahad S, Bajwa AA, Nazir U, Anjum SA, Farooq A, Zohaib A, et al. Crop production under drought and heat stress: plant responses and management options. Front Plant Sci. 2017. https://doi.org/10.3389/fpls.2017.01147.
Ibrahim EA. Seed priming to alleviate salinity stress in germinating seeds. J Plant Physiol. 2016. https://doi.org/10.1016/j.jplph.2015.12.011.
Yadav PV, Kumari M, Ahmed Z. Seed priming mediated germination improvement and tolerance to subsequent exposure to cold and salt stress in Capsicum. Res J Seed Sci. 2011. https://doi.org/10.3923/rjss.2011.125.136.
Chidambaranathan P, Jagannadham PTK, Satheesh V, Kohli D, Basavarajappa SH, Chellapilla B, et al. Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage. J Plant Res. 2018. https://doi.org/10.1007/s10265-017-0948-y.
Zhou M, Zheng S, Liu R, Lu J, Lu L, Zhang C, et al. Genome-wide identification, phylogenetic and expression analysis of the heat shock transcription factor family in bread wheat (Triticum aestivum L.). BMC Genomics. 2019. https://doi.org/10.1186/s12864-019-5876-x.
Zhang Q, Zhang WJ, Yin ZG, Li WJ, Zhao HH, Zhang S, et al. Genome- and Transcriptome-wide identification of C3Hs in common bean (Phaseolus vulgaris L.) and structural and expression-based analyses of their functions during the sprout stage under salt-stress conditions. Front Genet. 2020. https://doi.org/10.3389/fgene.2020.564607.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014. https://doi.org/10.1093/nar/gkt1223.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, et al. HMMER web server: 2015 update. Nucleic Acids Res. 2015. https://doi.org/10.1093/nar/gkv397.
Hoogland C, Mostaguir K, Appel RD, Lisacek F. The world-2DPAGE constellation to promote and publish gel-based proteomics data through the ExPASy server. J Proteome. 2008. https://doi.org/10.1016/j.jprot.2008.02.005.
Yao Q, Xu D. Bioinformatics analysis of protein phosphorylation in plant systems biology using P3DB. Methods Mol Biol. 2017. https://doi.org/10.1007/978-1-4939-6783-4_6.
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020. https://doi.org/10.1016/j.molp.2020.06.009.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018. https://doi.org/10.1093/molbev/msy096.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009. https://doi.org/10.1093/nar/gkp335.
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015. https://doi.org/10.1093/bioinformatics/btu817.
Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol. 2019. https://doi.org/10.1016/j.ympev.2018.10.001.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009. https://doi.org/10.1101/gr.092759.109.
Wang Y, Li J, Paterson AH. MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics. 2013. https://doi.org/10.1093/bioinformatics/btt150.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012. https://doi.org/10.1093/nar/gkr944.
Alsamir M, Mahmood T, Trethowan R, Ahmad N. An overview of heat stress in tomato (Solanum lycopersicum L.). Saudi. J Biol Sci. 2021. https://doi.org/10.1016/j.sjbs.2020.11.088.
Wang F, Chen X, Dong S, Jiang X, Wang L, Yu J, et al. Crosstalk of PIF4 and DELLA modulates CBF transcript and hormone homeostasis in cold response in tomato. Plant Biotechnol J. 2020. https://doi.org/10.1111/pbi.13272.
Mohammadi S, Pourakbar L, Siavash Moghaddam S, Popović-Djordjević J. The effect of EDTA and citric acid on biochemical processes and changes in phenolic compounds profile of okra (Abelmoschus esculentus L.) under mercury stress. Ecotoxicol Environ Saf. 2021. https://doi.org/10.1016/j.ecoenv.2020.111607.
Zhang Q, Zhang W-j, Yin Z-g, Li W-j, Xia C-Y, Sun H-Y, et al. Genome-wide identification reveals the potential functions of the bZIP gene family in common bean (Phaseolus vulgaris) in response to salt stress during the sprouting stage. J Plant Growth Regul. 2021. https://doi.org/10.1007/s00344-021-10497-x.
Zhao Q, Wang H, Du Y, Rogers HJ, Wu Z, Jia S, et al. MSH2 and MSH6 in mismatch repair system account for soybean (Glycine max (L.) Merr.) tolerance to cadmium toxicity by determining DNA damage response. J Agric Food Chem. 2020. https://doi.org/10.1021/acs.jafc.9b06599.
Zhang Q, Li M, Xia CY, Zhang WJ, Yin ZG, Zhang YL, et al. Transcriptome-based analysis of salt-related genes during the sprout stage of common bean (Phaseolus vulgaris) under salt stress conditions. Biotechnol Biotechnol Equip. 2021. https://doi.org/10.1080/13102818.2021.1954091.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−ΔΔC(T)) method. Methods. 2001. https://doi.org/10.1006/meth.2001.1262.
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